General information for g6855.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Rho guanine nucleotide exchange factor 4.
Parent gene
- The parent gene g6855 is located on chr_2: 19196278..19202766 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g6855 | g6855.t1 | isoform | g6855.t1 | 19194008 | 19202766 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon1 | 19194008 | 19195139 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS1 | 19194008 | 19195139 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon2 | 19195200 | 19195469 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS2 | 19195200 | 19195469 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon3 | 19195533 | 19196224 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS3 | 19195533 | 19196224 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon4 | 19196279 | 19196426 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS4 | 19196279 | 19196426 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon5 | 19196493 | 19196601 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS5 | 19196493 | 19196601 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon6 | 19196716 | 19196869 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS6 | 19196716 | 19196869 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon7 | 19202157 | 19202208 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS7 | 19202157 | 19202208 |
| chr_2 | g6855 | g6855.t1 | exon | g6855.t1.exon8 | 19202747 | 19202766 |
| chr_2 | g6855 | g6855.t1 | cds | g6855.t1.CDS8 | 19202747 | 19202766 |
| chr_2 | g6855 | g6855.t1 | TSS | g6855.t1 | NA | NA |
| chr_2 | g6855 | g6855.t1 | TTS | g6855.t1 | NA | NA |
Sequences
>g6855.t1 Gene=g6855 Length=2577
ATGTTCAACTCAACACACACAAATCTATCATCTGACACCAATGAATTATTGTCGATGTTT
CCTCCGCACACACCTCTTCAAATGCGAGCAGTTTCGAGTCCATCGCTAACAGAAAATCCT
GTAGAAAAATCACCTTCAAACAGCACATCACCAAAGTTCTCGATTAAGCCCGTACCAAAT
GGTCATACACAGAACCATATTGAATTGACTGATCGGAATCAAACAGGGTCCTCAGGTGTT
TTACAAAAATTTAAGAAGACATTTTCAAATTTTAAGAATGGAAAGACAACCGTACCAGTT
GCAAATGAAGAACAAAGCGATGCCAAACACCATCGATTTGGACCGTTAGTGTGGCGAACA
AGCAAAGAACGAAGAAAAACAAAGACACATAGACGCGACAAATGCAATTCCGGAGATTCT
GGCATTCAAGTTGAACTAGAGAATGATGAAAATTTGCCAGAAAATGTCTCACCACAGCAG
ATGGATATTTCACCGCAACTTAAAAGTAACAGTGCCAAAGTAAGACGTGCTAATAGTGCA
AAAGTTTCCACAACAACCAAATCAACAAAAAGCAGCTCAAAGCATTCAGCCAAATCAAAG
CGTTCACTAAGTCAACCGTCAGATTTAGATGTGATTGTGTGTGAAAGCAAAATGATGAGT
AATTTGGACGATATTAAGCACATTGATGATGATGATGATGCATCGGATACAGATAGTCTT
AGTTCAAATCATGTAGATGAAATGGATGAAGAAGAAATTCAGAAAAATGCTGTAGTTTAT
GCTGAAGTTCTCTATCAATTTAGAGCGGGTGGACCACAAGAATTATCGCTAGAGAAAGGA
ACATTAGTGGAGGTGATAAAACGTGAGACAGGCCCATGGTGGTGGGGACGAATAAAGTAT
GATGCTATTGTGAATGAAAGTGAACTTGAGATAAAGCAAGGATGGTTTCCTAAAGATTTT
GTAAAGGTGCTTCCCACATATGGAAATCGAAAATTTCTTCACCAACAATCATCAATCGAC
TGTGATATCAATAATACAATTCTACCACCATCAACTGCCGCACCAAGCATCTCTTCTAGT
CAATCAAATAGCGAAATAATGAGAGATAATGTCATCAAAGAATTGCTCGAGACAGAAATT
AATTATGTTAAGTTACTTAATTCACTTGTCAATGGATTTATAAAAGAAATGAAAGAACGA
TCTGATGTTTTCTCATTAGAAAGCATTTTCCTTTTGTTTTCAAATATCGAGCAAATCTAT
CGTTTTCAACAAAACTTTTTAGAGGCCCTTCGTATTGCCATTCCTAATGGAAGAATAGCA
GAAGTCTTTTTAGACTTTCAGTCAGCATTTATGGTTTACTCACAGTACTGCAACTCGTAT
CCAAGAGCTCTTATGGAGCTAGAAAACTTTTCGAATAATAAAGAAGCCACTGCAATATTA
GAAAGCTGTCGTATCGCACAAAATTTACCCGAATTACCATTATCAGCGCATTTATTAGCG
CCTATACAAAGAATTTGTCGATATCCTTTGCACTTAAGTGAACTTGTGAAACATTCAAAG
ACCCGCAAAGAAATTCTTCTTAAAATGGATGTGCATCAATTGAGTAAAAATGACCTTGAA
ACAATTGATTGTAAAGAAATGTTTGATCTGTCATTAAATGCAATGAAGCGAGTTACAGAG
ATGGTAAACGAAGGCAAAAGACATAGTGAATATTTATCGCGAATTCAAGCAAGATTTGAA
AATTTTCAAGGACCATCAATAAATCTGCATAGTACTAGACTTTTTCTTCAGACAGACGCA
ATTAGAGTGTCACCAAATCTATGGAATAATACTTATACACTCTTCTTATTTGATCGACAG
TTGGTGTATTGCAAAAAAGACCTTTTAAAGCGTACTAGCTACATCTACAAAGGACGAATA
TTTCTTGACAACTGTCGTATTCTCAATTTACCTGACGGTCGCATGTTTGGCGTCAATTTG
AAAAATGCTTTAAGAATATTTTGTGAAGCTCGTGGAAAATGGTTTGACTTTTGCTTCCGT
TCAAATTCAAGCAAGACGAGATTTCTCAATACGCTCTCAGCTGAAAGACAATTTTGCGGA
TCAAGTTTATTTGTGTCTGAAATTGCTTCCGGTTTGGACGATGATAATTTGTCAGATGAT
CAGAATGTACTAAATCTTAATTATGATGAGCGACCAATTGATGTTGAACATGGAGTAACT
GCAAATGGAAATTCTACACCAACAGAATCACCTTTAAAACAACAAAAATTTAGTGATTCA
TTGCCTAAAAAATCACGAAAATCTTCCAAAGAAGCGCCATCACAAATTATTATTGACTAC
AATCCTGCAGTAAGTTCTTCATCAAACAGACGTCGTCTTGGAAATTGGTTTAGAAAGTCA
AAGAGCACAAATAGTACACCATCACAAAGTCCAACTCATCATCCACTTGTTGCTACCGCT
ACTGTGCCATCAATTGTTAATCATTCAGACAGCAATTCATCATCACAGCAAAGTTCACCA
GTCAATTATCCTCGGCCAAAATTTAAAGAAGCCACTAGTGTTGGAGGATCGTCTTGA
>g6855.t1 Gene=g6855 Length=858
MFNSTHTNLSSDTNELLSMFPPHTPLQMRAVSSPSLTENPVEKSPSNSTSPKFSIKPVPN
GHTQNHIELTDRNQTGSSGVLQKFKKTFSNFKNGKTTVPVANEEQSDAKHHRFGPLVWRT
SKERRKTKTHRRDKCNSGDSGIQVELENDENLPENVSPQQMDISPQLKSNSAKVRRANSA
KVSTTTKSTKSSSKHSAKSKRSLSQPSDLDVIVCESKMMSNLDDIKHIDDDDDASDTDSL
SSNHVDEMDEEEIQKNAVVYAEVLYQFRAGGPQELSLEKGTLVEVIKRETGPWWWGRIKY
DAIVNESELEIKQGWFPKDFVKVLPTYGNRKFLHQQSSIDCDINNTILPPSTAAPSISSS
QSNSEIMRDNVIKELLETEINYVKLLNSLVNGFIKEMKERSDVFSLESIFLLFSNIEQIY
RFQQNFLEALRIAIPNGRIAEVFLDFQSAFMVYSQYCNSYPRALMELENFSNNKEATAIL
ESCRIAQNLPELPLSAHLLAPIQRICRYPLHLSELVKHSKTRKEILLKMDVHQLSKNDLE
TIDCKEMFDLSLNAMKRVTEMVNEGKRHSEYLSRIQARFENFQGPSINLHSTRLFLQTDA
IRVSPNLWNNTYTLFLFDRQLVYCKKDLLKRTSYIYKGRIFLDNCRILNLPDGRMFGVNL
KNALRIFCEARGKWFDFCFRSNSSKTRFLNTLSAERQFCGSSLFVSEIASGLDDDNLSDD
QNVLNLNYDERPIDVEHGVTANGNSTPTESPLKQQKFSDSLPKKSRKSSKEAPSQIIIDY
NPAVSSSSNRRRLGNWFRKSKSTNSTPSQSPTHHPLVATATVPSIVNHSDSNSSSQQSSP
VNYPRPKFKEATSVGGSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6855.t1 | CDD | cd00174 | SH3 | 260 | 320 | 2.17317E-11 |
| 12 | g6855.t1 | CDD | cd00160 | RhoGEF | 368 | 563 | 2.58861E-39 |
| 11 | g6855.t1 | CDD | cd01224 | PH_Collybistin_ASEF | 569 | 702 | 3.96315E-53 |
| 8 | g6855.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 248 | 324 | 6.4E-16 |
| 10 | g6855.t1 | Gene3D | G3DSA:1.20.900.10 | - | 347 | 584 | 3.3E-60 |
| 9 | g6855.t1 | Gene3D | G3DSA:2.30.29.30 | - | 587 | 708 | 9.9E-29 |
| 20 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 78 | - |
| 17 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 78 | - |
| 22 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 206 | - |
| 23 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 104 | 122 | - |
| 21 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 150 | 206 | - |
| 26 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 248 | - |
| 24 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 743 | 776 | - |
| 25 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 743 | 758 | - |
| 18 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 858 | - |
| 19 | g6855.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 843 | - |
| 3 | g6855.t1 | PANTHER | PTHR45834:SF3 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3, ISOFORM L | 101 | 832 | 1.8E-185 |
| 4 | g6855.t1 | PANTHER | PTHR45834 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9-RELATED | 101 | 832 | 1.8E-185 |
| 1 | g6855.t1 | Pfam | PF00018 | SH3 domain | 263 | 317 | 1.7E-5 |
| 2 | g6855.t1 | Pfam | PF00621 | RhoGEF domain | 371 | 524 | 8.2E-36 |
| 28 | g6855.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 256 | 326 | 21.461 |
| 27 | g6855.t1 | ProSiteProfiles | PS50010 | Dbl homology (DH) domain profile. | 367 | 565 | 31.115 |
| 14 | g6855.t1 | SMART | SM00326 | SH3_2 | 259 | 325 | 5.0E-11 |
| 15 | g6855.t1 | SMART | SM00325 | RhoGEF_3 | 371 | 564 | 2.3E-36 |
| 16 | g6855.t1 | SMART | SM00233 | PH_update | 588 | 699 | 0.0056 |
| 7 | g6855.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 257 | 326 | 7.35E-14 |
| 6 | g6855.t1 | SUPERFAMILY | SSF48065 | DBL homology domain (DH-domain) | 354 | 582 | 1.57E-46 |
| 5 | g6855.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 568 | 699 | 1.59E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
| GO:0005085 | guanyl-nucleotide exchange factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05769 (Rho guanine nucleotide exchange factor 4/29)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
